Projects:DicomToNrrdForDTI - Revision history

Sgouttard at 17:29, 29 April 2008

2008-04-29T17:29:06Z

Sgouttard at 17:17, 29 April 2008

2008-04-29T17:17:59Z

Sgouttard at 17:10, 29 April 2008

2008-04-29T17:10:57Z

Sgouttard at 17:03, 29 April 2008

2008-04-29T17:03:06Z

Sgouttard at 16:57, 29 April 2008

2008-04-29T16:57:04Z

Sgouttard at 16:56, 29 April 2008

2008-04-29T16:56:32Z

Sgouttard at 16:55, 29 April 2008

2008-04-29T16:55:41Z

Sgouttard at 16:50, 29 April 2008

2008-04-29T16:50:32Z

Sgouttard: New page: Dicom conversion for DTI data Here are a few notes about our observations on the conversion of DTI dicom data from a TimTrio scanner to volumes

2008-04-25T21:26:34Z

New page: Dicom conversion for DTI data Here are a few notes about our observations on the conversion of DTI dicom data from a TimTrio scanner to volumes

New page

Dicom conversion for DTI data

Here are a few notes about our observations on the conversion of DTI dicom data from a TimTrio scanner to volumes

← Older revision		Revision as of 17:29, 29 April 2008
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	=== Orientation ===		=== Orientation ===
		+
		+	All the information for the image orientation are included in the dicom header. They are used to create the Nrrd header to process the dwi images.
		+	When displaying the tensor we can see that the orientation is not correct. There is a flip along the X axis.
		+
		+	Here are the Nrrd header generated from dicom and its associated tensor visualization:`
		+
		+	<code><pre> NRRD0005
		+	# Complete NRRD file format specification at:
		+	# http://teem.sourceforge.net/nrrd/format.html
		+	type: short
		+	dimension: 4
		+	space: right-anterior-superior
		+	sizes: 26 96 96 81
		+	space directions: none (-1.97917,0,0) (0,-1.97917,0) (0,0,-2)
		+	kinds: list domain domain domain
		+	endian: little
		+	encoding: gzip
		+	space origin: (48,48,40.5)
		+	measurement frame: (1,0,0) (0,1,0) (0,0,1)
		+	modality:=DWMRI
		+	DWMRI_b-value:=1000.000000
		+	DWMRI_gradient_0000:=0.000000 0.000000 0.000000
		+	DWMRI_gradient_0001:=0.999310 -0.026261 -0.026261
		+	DWMRI_gradient_0002:=-0.935465 0.003956 -0.353397
		+	DWMRI_gradient_0003:=-0.935257 0.004295 0.353943
		+	DWMRI_gradient_0004:=-0.808036 0.528933 0.259437
		+	DWMRI_gradient_0005:=-0.576658 0.580108 -0.575274
		+	DWMRI_gradient_0006:=-0.577350 -0.584657 -0.569950
		+	DWMRI_gradient_0007:=-0.577350 -0.581504 0.573167
		+	DWMRI_gradient_0008:=-0.497275 -0.852931 0.158826
		+	DWMRI_gradient_0009:=-0.354696 0.934976 0.003268
		+	DWMRI_gradient_0010:=-0.355116 0.934819 0.002524
		+	DWMRI_gradient_0011:=0.309152 -0.857266 -0.411728
		+	DWMRI_gradient_0012:=0.305705 -0.000966 0.952126
		+	DWMRI_gradient_0013:=-0.307754 0.002441 0.951463
		+	DWMRI_gradient_0014:=0.002371 0.527850 0.849334
		+	DWMRI_gradient_0015:=0.001497 0.852692 -0.522412
		+	DWMRI_gradient_0016:=0.005889 0.359783 -0.933016
		+	DWMRI_gradient_0017:=0.002612 -0.359715 -0.933057
		+	DWMRI_gradient_0018:=-0.307108 -0.853200 -0.421585
		+	DWMRI_gradient_0019:=0.499156 0.528391 -0.686765
		+	DWMRI_gradient_0020:=-0.499365 0.528606 -0.686448
		+	DWMRI_gradient_0021:=0.496297 -0.854716 0.152151
		+	DWMRI_gradient_0022:=0.577350 -0.581702 -0.572966
		+	DWMRI_gradient_0023:=-0.807921 -0.529384 -0.258876
		+	DWMRI_gradient_0024:=-0.809373 -0.002040 0.587291
		+	DWMRI_gradient_0025:=-0.809376 -0.001631 -0.587289
		+	</pre></code>
		+
		+
		+	[[Image:TensorWrongOrientation.png\|thumb\|400px\|none\|Tensor display estimated straight from the dicom header information]]
		+
		+
		+	If we switch the “measurement frame” from (1,0,0) (0,1,0) (0,0,1) to (-1,0,0) (0,1,0) (0,0,1) (flipping the X axis) the tensors “look right” and we can track fibers.
		+
		+	[[Image:TensorRightOrientation.png\|thumb\|400px\|none\|Tensor display estimated with corrected Nrrd header]]
		+
		+	== Conclusion ==
		+
		+	We just wanted to point out here the differences between the information embedded in the dicom header and the one inputted in the scanner when the sequence is designed.

← Older revision		Revision as of 17:17, 29 April 2008
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	[[Image:BValComparison.png\|thumb\|400px\|left]]		[[Image:BValComparison.png\|thumb\|400px\|left]]
−	[[Image:BvalTable.png\|thumb\|300px\|right\|Bvalues comparison]]	+	[[Image:BvalTable.png\|thumb\|300px\|right\|none\|Bvalues comparison]]
		+
		+	=== Gradient directions ===
		+
		+	We noticed a major difference in the gradient direction encoding. When displaying the original vectors, they seem to be spread around the sphere. Whereas when we display the gradients of the dataset we worked with, they seem to be only on half of the plan. (in blue on the image)
		+
		+	[[Image:GradDirComp.png\|thumb\|400px\|left\|Dicom (blue) and Original (red) vectors displayed on the spehere]]
		+	[[Image:GradDir_lineComp.png\|thumb\|400px\|right\|Dicom (blue) and Original (red) lines displayed on the spehere]]
		+
		+	We know that it's not the vector itself which is important for the tensor computation, but more the line held by the vector. When we display lines instead of vectors, we can see that most of the blue lines have a matching red line. There is no more than 3 degrees difference between the vectors.
		+
		+	But the actual values read from the dicom being different from the original sequence could be an issues for some kind of DTI processing.
		+
		+
		+	=== Orientation ===

@@ Line 1: / Line 1: @@
-Dicom conversion for DTI data
+= Dicom conversion for DTI data =
@@ Line 10: / Line 10: @@
 The DTI sequence is a 25 directions with variable b-values plus one B0 image.
-[[Image:OrigDataBVal.png|400px|right]]
+[[Image:OrigDataBVal.png|thumb|400px|right]]
-[[Image:OrigGradDir3D.png|400px|left|none]]
+[[Image:OrigGradDir3D.png|thumb|400px|left|none|Original 25 gradient directions]]
@@ Line 19: / Line 19: @@
 We loaded this dicom dataset into the “Dicom DWI loader” module in Slicer3. This module creates a NRRD header based on the information read from the dicom header. We compared the values outputted by the Slicer3 modules with the ones gave to us by the people who designed the DTI sequence.
-= bValues =
+=== bValues ===

← Older revision		Revision as of 17:03, 29 April 2008
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	[[Image:OrigDataBVal.png\|400px\|right]]		[[Image:OrigDataBVal.png\|400px\|right]]
−	[[Image:OrigGradDir3D.png\|400px\|left]]	+	[[Image:OrigGradDir3D.png\|400px\|left\|none]]
		+
		+
		+
		+	== Data comparison ==
		+
		+	We loaded this dicom dataset into the “Dicom DWI loader” module in Slicer3. This module creates a NRRD header based on the information read from the dicom header. We compared the values outputted by the Slicer3 modules with the ones gave to us by the people who designed the DTI sequence.
		+
		+	= bValues =

← Older revision		Revision as of 16:57, 29 April 2008
Line 11:		Line 11:

	[[Image:OrigDataBVal.png\|400px\|right]]		[[Image:OrigDataBVal.png\|400px\|right]]
		+	[[Image:OrigGradDir3D.png\|400px\|left]]

← Older revision		Revision as of 16:56, 29 April 2008
Line 10:		Line 10:
	The DTI sequence is a 25 directions with variable b-values plus one B0 image.		The DTI sequence is a 25 directions with variable b-values plus one B0 image.

−	[[Image:OrigDataBVal.png\|~~200px~~\|~~Original bvalue sequence~~]]	+	[[Image:OrigDataBVal.png\|400px\|right]]

← Older revision		Revision as of 16:55, 29 April 2008
Line 9:		Line 9:

	The DTI sequence is a 25 directions with variable b-values plus one B0 image.		The DTI sequence is a 25 directions with variable b-values plus one B0 image.
		+
		+	[[Image:OrigDataBVal.png\|200px\|Original bvalue sequence]]

← Older revision		Revision as of 16:50, 29 April 2008
Line 1:		Line 1:
	Dicom conversion for DTI data		Dicom conversion for DTI data

−	~~Here are a few notes about our observations~~ on the conversion of DTI dicom data ~~from~~ a ~~TimTrio scanner to volumes~~	+
		+	== Introduction ==
		+
		+	In this page we present some results on the conversion from dicom data to DTI. Working with this new dataset, we noticed differences between the dicom header information and the ones from the original protocol designed for this study. In this page, we want describe and discuss these differences.
		+
		+	The data we worked with have been acquired with a Siemens 3T Tim Trio.
		+
		+	The DTI sequence is a 25 directions with variable b-values plus one B0 image.